Luebke K J, Landry S M, Tinoco I
Department of Chemistry, University of California at Berkeley, Berkeley, California 94720-1460, USA.
Biochemistry. 1997 Aug 19;36(33):10246-55. doi: 10.1021/bi9701540.
We present the solution conformation, determined by NMR spectroscopy, of a five-nucleotide RNA bulge loop. The bulge interrupts the stem of a 25-nucleotide RNA hairpin, and its sequence and flanking sequences are those of a conserved bulge from a Group I intron. The secondary structure of the bulge loop in the hairpin context is that predicted by the secondary structure prediction algorithm of Zuker. It differs, however, from the secondary structure deduced from sequence covariation of the bulge in the context of the functionally folded Group I introns and observed in the crystal structure of an independently folding domain of the Group I intron from Tetrahymena thermophila. This difference represents an exception to the heierarchical model of RNA folding in which preformed elements of secondary structure interact to form a tertiary structure. The three-dimensional structure of the bulge loop is characterized by discontinuous base stacking. Adjacent adenines stack with each other and with the flanking double helices. However, the position of the central uracil is not well defined by NOE distance constraints and is a point of discontinuity in the base stacking.
我们展示了通过核磁共振光谱法确定的一个五核苷酸RNA凸起环的溶液构象。该凸起打断了一个25核苷酸RNA发夹的茎，其序列和侧翼序列是来自I组内含子的保守凸起的序列。发夹结构中凸起环的二级结构是由祖克二级结构预测算法预测的。然而，它与从功能折叠的I组内含子背景下凸起的序列共变推导并在嗜热四膜虫I组内含子独立折叠结构域的晶体结构中观察到的二级结构不同。这种差异代表了RNA折叠层次模型的一个例外，在该模型中，预先形成的二级结构元件相互作用形成三级结构。凸起环的三维结构的特征是不连续的碱基堆积。相邻的腺嘌呤相互堆积并与侧翼双螺旋堆积。然而，中心尿嘧啶的位置没有被NOE距离约束很好地确定，并且是碱基堆积中的一个不连续点。
